I don't think you really have to pull them all the way through.
Just make sure the tapered end is pulled through so you are working with the main body of the zip-tie, where the thickness is constant (making for parallel faces).

Yep, that's a good tool.
Only complaint I have is that you have to carefully measure the the positions of the two end sliders when you clamp them down to make sure they are the same length, otherwise your flybar won't be level.
The sliders are indexed which is nice, but it takes a few minutes of trial-and-error to get it just right.
That said, once you get it set for a particular heli it is a solid tool.

I took mine to the local soccer field recently and had a minor spill halfway thru the first flight. Even w the tail slightly bent and the main gear missing a few teeth, it flew great! Made some odd clacking noise but once the rpm got up it was fine. I was quite surprised.